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Number of sequence provided in .data and .dist are not matching! #394

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Rmulet opened this issue Feb 6, 2024 · 0 comments
Open

Number of sequence provided in .data and .dist are not matching! #394

Rmulet opened this issue Feb 6, 2024 · 0 comments

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@Rmulet
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Rmulet commented Feb 6, 2024

Hi,

I have noticed that whenever I use seqDist with non-default options, seqCluster returns the following warning message.

In seqCluster(MixcrTest2, distMixcrTest2, .perc_similarity = 0.9) :
  Number of sequence provided in .data and .dist are not matching!

This happens, for example, if I pass only V.name to .group_by or CDR3.aa to .col (instead of CDR3.nt). In fact, this message appears in the Immunarch tutorial (https://immunarch.com/articles/web_only/clustering.html) when attempting to run the following two lines of code:

#calculate distance
distTCR <- [seqDist](https://immunarch.com/reference/seqDist.html)( TCRdata, .col = 'CDR3.aa')

#clustering TCR by CDR3 regions
clustTCR <- [seqCluster](https://immunarch.com/reference/seqCluster.html)(TCRdata, distTCR, .perc_similarity = 0.9)

What is the exact meaning of this warning? Is there any reason for concern or can we safely ignore it?

Thank you.

For the record, I installed Immunarch from Github, as it is not available on CRAN at the moment. But I doubt that's the reason because the same error appears on the website hosting the tutorial.

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